Quarto

Quarto - introduction

• Released in June 2022.
• Open-source scientific and technical publishing system.
• Facilitates the creation of dynamic, reproducible documents, presentations, and reports.
• Aims to produce high-quality, publication-ready outputs.
• Supports multiple programming languages including R, Python, and Julia.
• Enhances the reproducibility of scientific research.
• Allows embedding of source code in documents for transparency.

Historical development

• Evolution of Computational Document Authoring:

  • Before Quarto, R Markdown was a popular tool in the data science community for creating dynamic, reproducible documents using R. Increasing Demand for Multi-Language Support:

  • As the data science field grew, there was a rising demand for tools that could support multiple programming languages (e.g., Python, Julia) alongside R. Integration with Jupyter Ecosystem:

• Jupyter Notebooks gained popularity for interactive computing, creating a need for tools that could bridge R Markdown and Jupyter. Quarto’s Development:

• Quarto was developed to meet these evolving needs, offering a more flexible and powerful platform. It extended the capabilities of R Markdown by integrating with the Jupyter ecosystem and supporting multiple languages.

Benefits

• Enhanced Reproducibility in Scientific Research:

  • Facilitates the creation of documents where data, code, and narrative are closely intertwined.

  • Improves the transparency and verifiability of research findings.

• Easy Collaboration Features:

  • Supports collaborative workflows, making it simpler for teams to work together on documents.

  • Version control friendly, integrates well with platforms like GitHub.

• High-Quality Publishing Outputs:

  • Capable of generating documents in various formats including HTML, PDF, and Word.

  • Ensures professional-grade layout and typesetting for publication-ready outputs.

YAML header - 1

• Location and Structure:

  • At the top of the document, enclosed between --- lines.

  • Written in key-value pairs using YAML syntax.

• Document Metadata:

  • Title, author, and date.

  • Additional info like keywords and abstract.

• Format Specifications:

  • Determines output format (HTML, PDF, Word).

  • Customization options for each format.

• Code Chunk Options:

  • Global settings for all code blocks.

  • Controls echo, warning, message, and error displays.

YAML header - 2

• Table of Contents and Navigation:

  • Configuration of depth, appearance, and placement.

  • Section numbering enable/disable option.

• Citations and Bibliography:

  • Settings for citation processing.

  • Bibliography file specification and style guide selection.

• Language Settings:

  • Controls for multilingual document support.

• Cross-Referencing and Linking:

  • Configuration for figure and table referencing.

  • Hyperlinking and URL management settings.

Executable Code

#| echo: true
#| fig-width: 10
#| fig-height: 4.5
library(ggplot2)
ggplot(mtcars, aes(hp, mpg, color = am)) +
  geom_point() +
  geom_smooth(formula = y ~ x, method = "loess")

Demo

• in the existing quarto create a new code chunk
• copy the following code:

#| echo: true
#| fig-width: 10
#| fig-height: 4.5
library(ggplot2)
ggplot(mtcars, aes(hp, mpg, color = am)) +
  geom_point() +
  geom_smooth(formula = y ~ x, method = "loess")

• render the document. What can you observe?
• change the echo to false and render again.
• in YAML header add:

execution:
    echo: false

• render and observe. What changed?

Column Layout - 1

Arrange content into columns of varying widths:

::: columns
::: {.column width="35%"}
#### Motor Trend Car Road Tests

The data was extracted from the 1974 Motor Trend US magazine, and comprises fuel consumption and 10 aspects of automobile design and performance for 32 automobiles.
:::

::: {.column width="3%"}
:::

::: {.column width="62%"}
::: {.cell}
::: {.cell-output-display}
|                  |  mpg| cyl| disp|  hp|    wt|
|:-----------------|----:|---:|----:|---:|-----:|
|Mazda RX4         | 21.0|   6|  160| 110| 2.620|
|Mazda RX4 Wag     | 21.0|   6|  160| 110| 2.875|
|Datsun 710        | 22.8|   4|  108|  93| 2.320|
|Hornet 4 Drive    | 21.4|   6|  258| 110| 3.215|
|Hornet Sportabout | 18.7|   8|  360| 175| 3.440|
|Valiant           | 18.1|   6|  225| 105| 3.460|
:::
:::
:::
:::

Column Layout - 2

Demo

• to existing Quarto document add new header Columns
• create 2 columns, with 50 % and 50 % width
• in the first column add a code chunk:

airquality %>% 
   head() %>% 
   kable()

• in the second column add a code chunk:

airquality %>% 
   head() %>% 
   gt()

• render and observe

Interactive Slides

Include Jupyter widgets and htmlwidgets in your presentations